Because of its stem cell properties and numerous derivatives, the vertebrate neural crest (NC) represents an excellent system for examining questions of cell specification and differentiation during development. A gene regulatory network (GRN) defines the regulatory state of neural crest cells (Meulemans D & Bronner-Fraser M (2004) Dev Cell 7(3):291-299), such that modules of transcription factors function sequentially to first specify the neural plate border and then the nascent neural crest. The intricate regulatory interactions within the NC-GRN start with a group of transcription factors comprising an evolutionarily “inflexible” neural plate border regulatory unit, whose essential upstream function is to establish identity of the progenitor territory (Nikitina N, Sauka-Spengler T, & Bronner-Fraser M (2008) Proc Natl Acad Sci USA 105(51):20083-20088). Neural crest specifiers are genes responsible for formation of the neural crest. Sox10 is one of the earliest neural crest-specifying genes, driving delamination and directly regulating numerous downstream effectors and differentiation gene batteries. FoxD3 is one of the first markers of pre-migratory neural crest in many vertebrate species including mouse, chick, Xenopus and zebrafish (Hromas et al., 1999; Kos et al., 2001; Labosky and Kaestner, 1998; Lister et al., 2006; Pohl and Knochel, 2001; Sasai et al., 2001; Yamagata and Noda, 1998). Identification of region-specific regulatory elements as described herein, provides an important tool for identifying and manipulating the spatially-specified neural crest cells.